CW Survey of Sediment Quality SC R P in the Sacramento-San Joaquin Delta Es 9 tablished 196 Steven M. Bay Sarah Lowe Karen Gehrts SCCWRP Technical Report #686 Survey of Sediment Quality in the Sacramento-San Joaquin Delta Steven M. Bay1, Sarah Lowe2, and Karen Gehrts3 1Southern California Coastal Water Research Project, Costa Mesa, CA 2San Francisco Estuary Institute, Richmond, CA 3Department of Water Resources, Sacramento, CA June 2020 Technical Report 686 EXECUTIVE SUMMARY The area of the convergence of the Sacramento and San Joaquin Rivers in central California has been urbanized for over 100 years and it is impacted by multiple types of anthropogenic stressors. The Sacramento-San Joaquin River Delta (Delta) is formed by the confluence of the two rivers and by natural and man-made channels, wetlands, and levees. In the Delta, riverine freshwater and saltwater from the San Francisco Bay mix to create a rich habitat. The Delta is an area of great importance to humans because it is the center of California’s water distribution system and has significant cultural value. The intense uses of the Delta’s water and other anthropogenic modifications have stressed this ecosystem. Evidence of a stressed ecosystem has been found by multiple studies investigating the Delta’s pelagic organism decline (POD). According to POD studies, some fish species have low abundances and long-term declines in population numbers. Contaminants, in addition to other types of stressors, are thought to be important contributors to adverse ecological impacts in the Delta. Most contamination studies have investigated water column contaminants and little information is available to characterize the extent and impacts of sediment contamination. Understanding sediment quality in this area is of key importance because sediments play an important role in determining the fate and effects of contaminants in estuaries. The lack of sediment contaminant information for the Delta is a critical data gap to understanding ecological impacts in the Delta. The Delta Survey was conducted to characterize sediment quality in the Delta and its main tributaries. This survey investigated the presence and magnitude of sediment contamination, measured sediment toxicity, and characterized the benthic community in the Delta. The samples for this study were collected in 2007 and 2008. Potential temporal and spatial trends were investigated with the data generated. A total of 144 samples were collected during the Delta Survey, with analyses conducted following a tiered approach. First, all 144 samples were analyzed with a 10-day amphipod survival and growth test using Hyalella azteca. The benthic macrofauna at each station were identified and enumerated to characterize community composition. The initial toxicity results were used to select a subset of 75 sediment samples for further toxicity testing and chemical analysis. The second bioassay was a 10-day survival and growth test conducted with midge larvae (Chironomus dilutus (tentans)). Legacy (e.g., DDTs) and currently discharged contaminants (e.g., pyrethroid pesticides) were analyzed in the sediment to characterize chemical exposure. Chemical index analyses (e.g., Logistic Regression Modeling) were conducted to determine the sediment’s toxicity potential. The results of the Delta Survey showed widespread chemical contamination in sediments, but at relatively low concentrations. Sediment contaminants included metals, legacy trace organics, and current use pesticides. In general, there were few differences in chemical concentrations between sampling events. Some spatial trends in sediment contamination were observed. For example, higher levels of PAHs, DDTs, piperonyl butoxide, and diuron were present at the convergence of the Sacramento and San Joaquin Rivers. Higher PCB concentrations were observed in samples collected near Chipps Island and Stockton Channel when compared to concentrations found in other study areas. i Chemical index analyses indicated that there was low potential for toxicity associated with sediment contamination in the Delta. Analyses of acid volatile sulfides (AVS) and simultaneously extracted metals (SEM) indicated low bioavailability and potential for toxicity from divalent metals such as copper, cadmium, and mercury. Toxic units (TUs) were calculated for PAHs and pyrethroids and showed that sediment concentrations of these contaminants had little toxic potential. Only 1% of the sediments tested had pyrethroid TUs that could potentially cause toxicity. Characterization of overall chemical exposure using the California Logistic Regression Model index (CALRM) also showed that most of the sediments collected in the Delta Survey had low toxicity potential. The CALRM classified most sediment samples as providing minimal or low chemical exposure with regards to the likelihood of observing biological effects. Exposure to Delta sediments caused little mortality in either of the toxicity tests conducted. However, sublethal responses such as decreased growth or biomass were observed in both amphipods and midges. Sublethal effects were found during both sampling events, but no specific patterns were observed. During the first sampling event (2007) sediments from 10 to 14% of the stations caused a decrease in either growth or biomass of one of the species. No sublethal effects were observed in amphipods exposed to 2008 sediment samples. In contrast, C. dilutus showed decreased growth or biomass when exposed to sediments from 24% of the stations sampled in 2008. There was little indication of a higher prevalence of toxicity in specific areas of the Delta. Some toxicity was observed in sediments from stations located in slough areas and channels; however, most of the stations exhibited no toxicity to either test species. In only one case was toxicity detected in samples collected at the same station during both sampling events. The benthic species collected during the Delta Survey were representative of a tidal freshwater assemblage and dominated by annelids, arthropods, and mollusks. The two species most commonly found were the freshwater clam Corbicula fluminea (90% of the samples) and the oligochaete worm Limnodrilus hoffmeisteri (80% of the samples). Approximately 17% of the taxa were non-indigenous, including dominant species such as C. fluminea and the amphipod Gammarus daiberi. The freshwater polychaete worm Manayunkia speciosa had the highest average abundance among the samples. Some temporal shifts in dominant macrobenthic taxa were found. Annelids accounted for 98% of the total abundance in 2007, while arthropods accounted for 99% of the total abundance in 2008. However, there were no differences in mean total abundance or mean number of taxa between 2007 and 2008. There were spatial differences in species composition which reflected three sub- habitat types. These sub-habitats were: main and open channels dominated by amphipods (Americorophium spp., G. daiberi), smaller cross-channels and back bays dominated by M. speciosa and G. daiberi, and the more distal freshwater channels dominated by oligochaetes. However, the dominant fauna among these sub-habitats had 50 to 60% similarity. The Delta Survey provides some of the most comprehensive data to date to investigate the quality of the sediments in the Sacramento-San Joaquin Delta. The results indicate that most of the area surveyed had good sediment quality with respect to impacts from chemical contamination. This conclusion is supported by the presence of only low levels of sediment toxicity and multiple chemical indices that indicate low toxicity potential. There were no clear relationships between the chemical concentrations and sediment toxicity. The cause of the mortality and the sublethal effects from the toxicity tests cannot be attributed to specific ii compounds with the results of this study. Further research is needed to evaluate whether Delta macrobenthic communities are impacted by the relatively low levels of sediment contaminants detected in the Delta ecosystem. ACKNOWLEDGEMENTS Partial funding for this study was provided by the State Water Resources Control Board (SWRCB) as part of the Sediment Quality Objectives (SQO) program (under agreement number 08-061-250). This study was also funded in part by in-kind services from the Interagency Ecological Program (IEP) participants: the U.S. Bureau of Reclamation and the California Department of Water Resources (DWR)-Environmental Monitoring Program (EMP). We thank former SCCWRP staff Doris Vidal-Dorsch and A. Elizabeth Fetscher for their many contributions to data analysis and writing of the report. The authors would like to thank Paul Salop from Applied Marine Sciences, Livermore, California, for coordinating the field sampling and sample handling. The authors would also like to thank the U.S. Bureau of Reclamation for the use of the vessel Endeavour and its skipper Nick Sakata. The authors would also like to recognize the individuals and agencies that performed sample analyses: Brian Anderson and Bryn Phillips of University of California Davis Marine Pollution Studies Laboratory; Colin Davies and Elizabeth Madonick of Brooks Rand Laboratory, LLP; Dave Crane of the California Department of Fish and Game; Ken Davis of Applied Marine Sciences, Inc., Texas; Greg Salata of Columbia Analytical Services, Inc.; and Wayne Fields of Hydrozoology. We also thank Bruce Thompson from SFEI for his contribution to the description of the benthic community composition in this report. This report was originally